Sunda Strait is an important passage for the Java Sea water to flow into the Indian Ocean. There is Java sea in North close to Karimata Strait and Eastern Indian Ocean in South part. Headed from north to south of Sunda Strait, has a high primary productivity that signifies the fertility of water. The strong El Nino (SOI) in 2015, hypothesized to affect variability values of a-chlorophyll content and sea surface temperature in this area. The research aims to know the distribution pattern of chlorophyll-a, and sea surface temperature due to El Nino effect on transition season I (March, April and May 2015). The relationship of both with SOI was analyzed by simple linear correlation analysis. The results showed that the distribution of chlorophyll-a in Northen Sunda Strait is not affected by El Nino but comes from the mouth of the Musi River. The pattern of sea surface temperature distribution from Northern to Southern of Sunda Strait showed in this area affected by El Nino so that the temperature is cooler. The relationship of chlorophyll-a with SOI has a negative moderate correlation (-0.532), indicating that chlorophyll-a in this waters have the direction opposite to SOI and sea surface temperature with SOI has a strong positive correlation (of 0.959).